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Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KCE PDB entry 1KCE with waters and ligands removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.1 298 potassium phosphate, EDTA, ammonium sulfate, DTT, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.1 α = 90 b = 127.1 β = 90 c = 68.1 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS II monochromater 1998-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 40 100 0.174 8.1 8.7 24679 24679 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.55 100 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1KCE with waters and ligands removed 2.4 36.69 -3 24679 24679 1694 100 0.1913 0.187 0.187 0.246 RANDOM 34.2
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.95 0.26 -1.95 3.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 5.09 c_mcangle_it 4.71 c_scbond_it 3.38 c_mcbond_it 3.15 c_angle_deg 1.6 c_improper_angle_d 0.94 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4300 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 110
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing